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SAMtool  

Stock Assessment Methods Toolkit
View on CRAN: Click here


Download and install SAMtool package within the R console
Install from CRAN:
install.packages("SAMtool")

Install from Github:
library("remotes")
install_github("cran/SAMtool")

Install by package version:
library("remotes")
install_version("SAMtool", "1.9.2")



Attach the package and use:
library("SAMtool")
Maintained by
Quang Huynh
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-01-22
Latest Update: 2025-04-28
Description:
Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform data-rich fisheries. 'SAMtool' provides a conditioning model, assessment models of varying complexity with standardized reporting, model-based management procedures, and diagnostic tools for evaluating assessments inside closed-loop simulation.
How to cite:
Quang Huynh (2021). SAMtool: Stock Assessment Methods Toolkit. R package version 1.9.2, https://cran.r-project.org/web/packages/SAMtool. Accessed 29 Oct. 2026.
Previous versions and publish date:
(2026-07-09 08:24), 1.0.0 (2021-01-22 09:50), 1.1.0 (2021-02-02 11:20), 1.1.1 (2021-02-17 12:50), 1.1.2 (2021-03-09 21:30), 1.2.0 (2021-07-06 08:30), 1.2.1 (2021-08-12 08:10), 1.2.2 (2021-09-16 23:20), 1.2.3 (2021-11-28 16:50), 1.2.4 (2021-12-15 01:20), 1.2.5 (2022-01-12 11:22), 1.2.6 (2022-03-31 14:00), 1.3.0 (2022-04-08 09:02), 1.3.1 (2022-05-06 09:00), 1.4.0 (2022-06-07 23:50), 1.4.1 (2022-11-16 13:11), 1.5.0 (2023-01-29 07:50), 1.5.1 (2023-02-09 00:20), 1.5.2 (2023-04-05 01:10), 1.5.3 (2023-05-23 20:42), 1.6.0 (2023-07-19 18:40), 1.6.1 (2023-08-23 04:30), 1.6.2 (2023-10-26 10:30), 1.6.3 (2023-11-18 06:50), 1.6.4 (2024-02-15 21:10), 1.7.0 (2024-08-29 20:00), 1.8.0 (2024-11-08 00:50), 1.8.1 (2025-04-29 00:30), 1.8.2 (2025-09-05 19:10), 1.9.0 (2025-10-21 07:10), 1.9.1 (2026-01-15 07:11)
Other packages that cited SAMtool R package
View SAMtool citation profile
Other R packages that SAMtool depends, imports, suggests or enhances
Complete documentation for SAMtool
Functions, R codes and Examples using the SAMtool R package
Some associated functions: Assessment-class . DD_TMB . HCR_FB . HCR_MSY . HCR_escapement . HCR_fixedF . HCR_ramp . HCR_segment . HCRlin . Model-based-MP . PRBcalc . Probs . RCM . RCM2MOM . RCM_assess . RCMdata-class . RCModel-class . SAMtool-package . SCA . SCA_CAL . SCA_DDM . SCA_RWM . SP . SP_production . SSS . Shortcut . TAC_MSY . VPA . cDD . compare_models . diagnostic . getinds . mahplot . make_MP . pcod . plot.Assessment . plot.RCModel . plot.prof . plot.retro . plot_SR . plot_betavar . plot_composition . plot_crosscorr . plot_lognormalvar . plot_residuals . plot_steepness . plot_timeseries . posterior . prelim_AM . prof-class . profile . project-class . projection . retro-class . retrospective . retrospective_AM . sim-class . simulate . summary.Assessment . swordfish . userguide . 
Some associated R codes: Ancillary_Indicators.R . HCRs.R . Misc_fun.R . RCM2MOM.R . RCM_assess.R . RCM_data.R . RCM_est.R . RCM_int.R . RCM_rmd.R . SAMtool-package.R . assess_DD.R . assess_SCA.R . assess_SCA_ext.R . assess_SP.R . assess_SSS.R . assess_VPA.R . assess_cDD.R . assess_shortcut.R . define_S4_class_RCModel.R . define_S4_class_assess_RCMdata.R . define_S4_class_profile.R . define_S4_class_project.R . define_S4_class_retro.R . define_S4_generic_RCM.R . define_S4_generic_posterior.R . define_S4_generic_simulate.R . diagnostic.R . document_data.R . interim_MP.R . report_DD_TMB.R . report_SCA.R . report_SP.R . report_SSS.R . report_VPA.R . report_auxiliary.R . report_cDD.R . report_spict.R . retrospective_AM.R . rmd_report.R . z_MPs.R . zzz.R .  Full SAMtool package functions and examples
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